Creating an implant for spinal surgery - workflow questions
Hopefully this is captures the problem and a solution. 

To create geometry for a fixure which can be lifted off a complex geometry like a spine, you can use a high resolution mesh and the shrinkwrap modifier. The resulting object should be 'water-tight' and able to be 3D printed.







Detailed instructions:


Import the spine geometry.

Add a plane which will be the dividing plane between the upper and lower clamps.

Select the spine and the plane. Use ctrl-J to join the geometry. 
Add a cube for the upper portion of the clamp. Size it so it covers the area to the clamped. Keep it above the spline. This block should NOT intersect the spine geometry.

Select the cube and use tab to enter the 'edit mode'. In the edit mode, select the vertices on the bottom of the cube. Use subdivide to create a high resolution mesh on the bottom of the cube. With the bottom of the cube selected, add a vertex group and name it 'bottom'.

Use tab to return to object mode.
Add a shinkwrap modified to the cube. Project the shrinkwrap modified in the 'z' direction and only shinkwrap the 'bottom' vertex group. Set the spine as the target. This will project all of the vertices in the bottom group down onto the spine. Because the plane was added earlier, the shrinkwrap will either touch the bone or the separation plane. Since the vertices only project downward, the block can be removed by lifting off the spine.

You are done! Some other things to consider are increasing the mesh resolution in areas of interest to better match the scanned geometry and adding offset to the meshes to provide some fitting tolerance for installing and removing the blocks.






If additional clearance is needed between the scanned spine and the mold, the diplace modifier can be applied to the geometry. This will project the surfaces of the bones outward a little and give additional room. The image below shows the original spine in geometry as a solid and the displaced geometry in the wire mesh.